[2024-01-24 14:46:57,404] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:57,406] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:57,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg53a49aef-fd41-4b9a-a515-a738a52a8d3e/dqc_reference
[2024-01-24 14:46:58,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,642] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,642] [INFO] Running command: gunzip -c /var/lib/cwl/stga9c249b4-42c5-4646-a1ad-1410f5705eb7/GCF_900258035.1_LMG28615_genomic.fna.gz | prodigal -d GCF_900258035.1_LMG28615_genomic.fna/cds.fna -a GCF_900258035.1_LMG28615_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:21,801] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:21,801] [INFO] Task started: HMMsearch
[2024-01-24 14:47:21,801] [INFO] Running command: hmmsearch --tblout GCF_900258035.1_LMG28615_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53a49aef-fd41-4b9a-a515-a738a52a8d3e/dqc_reference/reference_markers.hmm GCF_900258035.1_LMG28615_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:22,154] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:22,156] [INFO] Found 6/6 markers.
[2024-01-24 14:47:22,214] [INFO] Query marker FASTA was written to GCF_900258035.1_LMG28615_genomic.fna/markers.fasta
[2024-01-24 14:47:22,215] [INFO] Task started: Blastn
[2024-01-24 14:47:22,215] [INFO] Running command: blastn -query GCF_900258035.1_LMG28615_genomic.fna/markers.fasta -db /var/lib/cwl/stg53a49aef-fd41-4b9a-a515-a738a52a8d3e/dqc_reference/reference_markers.fasta -out GCF_900258035.1_LMG28615_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:23,357] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:23,360] [INFO] Selected 17 target genomes.
[2024-01-24 14:47:23,361] [INFO] Target genome list was writen to GCF_900258035.1_LMG28615_genomic.fna/target_genomes.txt
[2024-01-24 14:47:23,375] [INFO] Task started: fastANI
[2024-01-24 14:47:23,375] [INFO] Running command: fastANI --query /var/lib/cwl/stga9c249b4-42c5-4646-a1ad-1410f5705eb7/GCF_900258035.1_LMG28615_genomic.fna.gz --refList GCF_900258035.1_LMG28615_genomic.fna/target_genomes.txt --output GCF_900258035.1_LMG28615_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:58,733] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:58,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53a49aef-fd41-4b9a-a515-a738a52a8d3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:58,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53a49aef-fd41-4b9a-a515-a738a52a8d3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:58,749] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:58,749] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:58,750] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Caballeronia novacaledonica	strain=LMG 28615	GCA_900258035.1	1544861	1544861	type	True	100.0	2220	2223	95	conclusive
Caballeronia temeraria		GCA_001544795.2	1777137	1777137	type	True	89.746	1712	2223	95	below_threshold
Caballeronia zhejiangensis	strain=OP-1	GCA_000698575.1	871203	871203	type	True	89.7002	1673	2223	95	below_threshold
Caballeronia glebae		GCA_001545035.2	1777143	1777143	type	True	89.6421	1637	2223	95	below_threshold
Caballeronia calidae		GCA_900044055.2	1777139	1777139	type	True	89.5326	1661	2223	95	below_threshold
Caballeronia pedi		GCA_001544915.2	1777141	1777141	type	True	89.4934	1748	2223	95	below_threshold
Caballeronia fortuita		GCA_001544835.2	1777138	1777138	type	True	89.3139	1634	2223	95	below_threshold
Caballeronia catudaia		GCA_001544755.2	1777136	1777136	type	True	89.0637	1639	2223	95	below_threshold
Caballeronia arvi		GCA_001544695.2	1777135	1777135	type	True	88.9053	1721	2223	95	below_threshold
Caballeronia cordobensis		GCA_001544575.2	1353886	1353886	type	True	88.7433	1688	2223	95	below_threshold
Caballeronia cordobensis	strain=LMG 27620	GCA_001278535.1	1353886	1353886	type	True	88.6671	1727	2223	95	below_threshold
Caballeronia ptereochthonis		GCA_001545075.2	1777144	1777144	type	True	88.4735	1605	2223	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	81.5525	1193	2223	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.3844	1049	2223	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	81.2717	985	2223	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	80.6514	1029	2223	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	80.594	1069	2223	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:58,751] [INFO] DFAST Taxonomy check result was written to GCF_900258035.1_LMG28615_genomic.fna/tc_result.tsv
[2024-01-24 14:47:58,752] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:58,752] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:58,752] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53a49aef-fd41-4b9a-a515-a738a52a8d3e/dqc_reference/checkm_data
[2024-01-24 14:47:58,754] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:58,826] [INFO] Task started: CheckM
[2024-01-24 14:47:58,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900258035.1_LMG28615_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900258035.1_LMG28615_genomic.fna/checkm_input GCF_900258035.1_LMG28615_genomic.fna/checkm_result
[2024-01-24 14:49:03,975] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:03,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:03,999] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:03,999] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:04,000] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900258035.1_LMG28615_genomic.fna/markers.fasta)
[2024-01-24 14:49:04,000] [INFO] Task started: Blastn
[2024-01-24 14:49:04,000] [INFO] Running command: blastn -query GCF_900258035.1_LMG28615_genomic.fna/markers.fasta -db /var/lib/cwl/stg53a49aef-fd41-4b9a-a515-a738a52a8d3e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900258035.1_LMG28615_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:06,031] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:06,036] [INFO] Selected 11 target genomes.
[2024-01-24 14:49:06,036] [INFO] Target genome list was writen to GCF_900258035.1_LMG28615_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:06,049] [INFO] Task started: fastANI
[2024-01-24 14:49:06,050] [INFO] Running command: fastANI --query /var/lib/cwl/stga9c249b4-42c5-4646-a1ad-1410f5705eb7/GCF_900258035.1_LMG28615_genomic.fna.gz --refList GCF_900258035.1_LMG28615_genomic.fna/target_genomes_gtdb.txt --output GCF_900258035.1_LMG28615_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:29,548] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:29,563] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:29,564] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900258035.1	s__Caballeronia novacaledonica	100.0	2220	2223	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000648925.1	s__Caballeronia jiangsuensis	92.2489	1757	2223	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	96.41	96.41	0.81	0.81	2	-
GCA_001544655.2	s__Caballeronia turbans	91.4658	1664	2223	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001580565.1	s__Caballeronia megalochromosomata	91.091	1694	2223	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000698575.1	s__Caballeronia zhejiangensis	89.7061	1671	2223	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	99.44	99.18	0.93	0.92	4	-
GCF_018408855.1	s__Caballeronia sp018408855	89.6803	1787	2223	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	98.23	98.23	0.88	0.88	2	-
GCF_001545035.1	s__Caballeronia glebae	89.6762	1633	2223	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900044055.2	s__Caballeronia calidae	89.5422	1661	2223	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544915.2	s__Caballeronia pedi	89.5031	1747	2223	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544695.2	s__Caballeronia arvi	88.8968	1722	2223	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544575.2	s__Caballeronia cordobensis	88.7485	1687	2223	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	98.18	97.54	0.94	0.91	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:29,568] [INFO] GTDB search result was written to GCF_900258035.1_LMG28615_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:29,569] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:29,572] [INFO] DFAST_QC result json was written to GCF_900258035.1_LMG28615_genomic.fna/dqc_result.json
[2024-01-24 14:49:29,572] [INFO] DFAST_QC completed!
[2024-01-24 14:49:29,573] [INFO] Total running time: 0h2m32s